Reliable estimation of nutrient concentrations is required to manage animal manure for protecting waters while sustaining crop production. This study was conducted to investigate sample variability and reliable nutrient analysis for several manure types and handling systems. Serial samples were collected from dairy, swine, and broiler poultry operations while manure was being loaded onto hauler tanks or spreaders for field application. Samples were analyzed for total solids (TS), total nitrogen (N), ammoniacal nitrogen (NH4-N), total phosphorus (P), and potassium (K). The least number of samples needed for reliable testing of total N and P, defined as +/- 10% of the experimental means with 99% probability, was obtained for each farm using a computer-intensive random resampling technique. Sample variability within farms, expressed as the coefficient of variation (CV), was mostly 6 to 8% for farms that used agitation of manure storages but several times higher (20-30%) on farms where no agitation was applied during the sampling period. Results from the random resampling procedure indicated that for farms that used agitation, three to five samples were adequate for a representative composite for reliable testing of total N and P; whereas for farms without agitation, at least 40 samples would be required. Data also suggest that using book values for manure nutrient estimations could be problematic because the discrepancies between book standards and measured farm data varied widely from a small amount to several fold.